Self-reflection in maths and chemistry

This reflection is an update from my previous one and a marker to see where I have improved and what I have done since writing my last reflection to today in order to help achieve progression.  As mentioned before both maths and chemistry play an important part in the fundamentals module and it is key to have a good foundation in both these subjects, and to use this a foundation to build from in further studies and more complex modules at uni.

In my last reflection I mentioned that my weak spot in the maths side of things was the calculations. I remember at the beginning of the module I struggled with some of the maths calculations and problems because they seemed complex and I had not used my maths skills for over two years before hand. Some of the calculations confused me and I did not know where to start. This was because of the layout of the questions and because I had not seen any questions like this before or had to solve them in the past.  To help myself understand the maths calculations and try to be able to solve them easily I used a book called “core maths for the biosciences” (Reed, 2011) This book was recommended by the teachers I class and was also available on loan in the university library. I found it useful as it had maths problem in it which were then explained and broken-down step by step. This gave me an understanding of how to tackle and solve problems that are given to me in class in the future.

In the last semester I have learnt not to be disheartened or become negative if I can’t solve a question, but instead to come away from it; have a break and put my mind a rest and them come back to the same thing with a different strategy and in a new light.  This is because people get so overworked over solving a problem they get frustrated and use them same strategy time and time again even though it wont work. (McLeod, 1989)

Chemistry was one of my weak spots during the begging of the first semester because I had not done any work on it since my gcse level studies at school and even then, found it more challenging because of its in-depth nature. If we look back at my first reflective piece we can see that I found it very daunting at first and struggled with the molecular and bonding sides of chemistry.  I mentioned I wanted to spend some time doing personal studies around this area to try and get myself up to scratch and ready for when things progressed in the module.  Since writing my last reflective piece I have managed to use some of my time to study and try and learn more around lessons to become more comfortable in myself.  Again, like the maths a good book was mention and recommended by the teachers for learning and self-teaching chemistry for this module. The book was available at the uni library for loan. I found it useful as it very good illustrated pictures which helped me to understand things better seeing it in this light. Molecular chemistry was explained nicely and bodning too, it was all broke down into bitesize pieces which helped me understand it better when next mentioned in class. (Crowe and Bradshaw, 2014)

Although I had a good book and found some good websites I could use for my personal studies on chemistry I found that I was not very good at time management and would always delay and avoid doing any studies in this area. I looked up ways to control and set up a time management programme in order to sort resolve this issue and hopefully improve my studies. I set aside scheduled slots of time for certain things and made sure when I was studying I was away from distractions and in the right frame of mind. There is no point going to study when you are stressed over tired or when your glued to your favourite series or social media. (PsycNET Record Display, 1990)

 

Looking back over the last semester I can see how I have improved in both maths and chemistry. I have been able to solve maths problems very quickly and easily by then end of the semester which I would have previously struggled with. Now I know not to overthink the problems when I first see them, and I can figure out where to start in solving the problem and what calculations to use; I m now confident and have little issues with my maths skills for this level of my studies in my course. Looking back at my chemistry progression I can also see an improvement, I no longer seem to daunt it and feel a lot more comfortable with it. Using my free time to pick up my weakness in this has benefited me and using time management plan has allowed me to put more time aside for studding and allowed to me to explore my potential.

 

 

Targets for the future are:

  • to continue with personal studies and try to find more in-depth resources rather than just the books mentioned in class or basic websites.
  • To continue using time management plan and excel in self-taught things
  • To try and maximise my studying and read up before classes so as to be ahead and maxims learning in class
  • To continue solving maths calculations so as not to challenge myself become rusty in the future and start over again.

 

 

 

References

Crowe, J. and Bradshaw, T. (2014) Chemistry for the biosciences: the essential concepts.

McLeod, D. B. (1989) ‘The Role of Affect in Mathematical Problem Solving.’ In Affect and Mathematical Problem Solving. Springer, New York, NY, pp. 20–36.

PsycNET Record Display – PsycNET (1990). [Online] [Accessed on 10th January 2018] /record/1991-13852-001.

Reed, M. B. (2011) core maths for the biosciences.

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Lab Report

DNA fingerprinting using PCR

Introduction:

DNA fingerprinting is a technique based on PCR amplification and restriction of DNA strands. (Vos et al., 1995) This method is used in forensics today and this practical is based on that. The method is helping solve murder and rape trials and convictions today as DNA of high molecular weight can be isolated from blood or semen of up to 4 years old. (Gill et al., 1987) The experiment being carried out is based on the use in forensics and we are going to try and match the suspect to the crime scene. We are however going to be using a pre-made kit with DNA samples in.

Experiment:

  • To carry out an experiment based on DNA fingerprinting using PCR and DNA amplification; using a ready-made kit with crime scene and four suspects.

 

  • To make our own gel for the electrophoresis stage of the practical.

 

Materials / Equipment:

  • DNA fingerprinting kit
  • PCR machine
  • 5x PCR tubes
  • Fine pen
  • Micro pipette
  • EdvoBeads
  • Centrifuge
  • Ice block
  • Distilled water

 

For making gel:

 

  • TBE buffer
  • Agarose powder
  • Microwave
  • beaker
  • Heat proof flask
  • Balance
  • Weighing boat
  • Conical flask
  • Gel mould and comb
  • Distilled water
  • spectrophotometer

 

Procedure:

The fist step of this practical was to get the samples of DNA ready for the PCR. We had the kit and had to complete a list of steps. There was four suspects DNA and then one crime scene, so we had to have five PCR tubes labelled for this and ready in an ice block for loading.

The second step was to put 20 ul of a primer mix from the kit into each tube and then to put 5 ul of each suspect DNA into the corresponding labelled tube and the same for the crime scene. We did this very accurately using a micro pipette and made sure to change the tip each time so not to contaminate anything and mess up the results.  After each tube was loaded an EdvoBead was added to each one and the tubes were gently flicked in order to dissolve the bead.

The third step was to centrifuge the tubes to collect samples at the bottom of them. Each tube was loaded correctly, and a sixth tube filled with water to match the weight of the others was added as a balance to make sure the centrifuge was weighted evenly.

After the centrifuge the tubes were ready to be loaded into the PCR machine. The PCR takes a while, so it gave us time to make our gels for the electrophoresis.

Making the gel:

The firsts step in making the gel was to weigh out 0.25g of agarose powder by using a balance and weighing boat.

Second step was to rinse the powder out of the weighing boat using the TBE buffer into a conical flask. The buffer was already measured to the right amount.

After both the powder and buffer were in a conical flask it was microwaved for 2 minutes, once done it was took out using the heat proof gloves so as not to burn yourself and then gently stirred to fully dissolve the powder.

The flask was then left to cool and once cooled to around 60 degrees 2.5 ul of safe view was added and the flask was swirled in order to mix it.

The gel was now ready to be put into the mould, it was gently poured in trying not to make any bubbles. Once loaded the comb was inserted in order to make the wells for loading at a later stage.  We used a 7×7 mould tray for the gel.

Once gel had set a diluted buffer was tipped over it, just enough to cover it.

Electrophoresis:

The final step of the practical was to run the samples through electrophoresis using the gel we made. Once the gel was cooled and set we took out the comb and then was ready to load our samples.

Our samples at this point have just finished PCR and are put back into the ice blocks. 5ul of loading solution was added to each of the five samples in preparation for electrophoresis. Once this had been done 25ul of each sample was loaded into individual wells in the gel. A ladder was also added into one of the wells.

Once all samples were loaded in the correct order the lid was put over the electrophoreses chamber and the wires were attached and we ran it for thirty minutes. Once the time was up the gel was put into a spectrophotometer which produces an image for analysing and discovering the results.

 

Results:

Our results came as a picture produced by the spectrophotometer and we analysed it from what we saw. The picture is as shown below in figure 1.  Our results and the image produced however did not turn out as planned and wasn’t a very good representative as we couldn’t really see or make out what was going on. We worked out that we left the electrophoresis to run for too long meaning that the samples had run to far and the gel had got disfigured. We were unable to compare the suspects to the crime scene because of this matter.

Figure 2 shows a good example of what we hoped to achieve and what the results would have looked like of we left it to run for a shorter time. The figure clearly demonstrates how you can link the suspect to the crime scene as the bands will line up and show a positive correlation.

 

dna pic 2.png
(figure 2)      (FDRSummerDrugs – Nucleic Acids (HL), 2014)
dna pic 1
(figure 1)

 

 

 

 

 

 

Conclusions:

From this practical I have learnt a lot; I have had to use many of my skills in order to complete it and get some form of result. The skills used were pipetting and weighing and I had to do perform these skills in an accurate way in order to achieve good results. The practical was a success and produced results meaning that my lab skills were proven to be accurate and that I did not contaminate any of the samples.

The negative was that the result was distorted, and we could not make up a conclusion of what suspect matched the crime scene. This was because we left the electrophoresis run for too long and it made the gel distort and the samples run of the end.

If I was to complete this practical again I would make sure to run the gel for maybe half the time so for fifteen minutes or I would use a longer gel mould to achieve a greater image to analyse. I would carry out the same skills and use the same equipment as I have not managed to find any issues or anomalies with the equipment or skills I used for other pars of the practical.

 

References

FDRSummerDrugs – Nucleic Acids (HL) (2014). [Online] [Accessed on 10th January 2018] https://fdrsummerdrugs.wikispaces.com/Nucleic+Acids+%28HL%29.

Gill, P., Lygo, J. E., Fowler, S. J. and Werrett, D. J. (1987) ‘An evaluation of DNA fingerprinting for forensic purposes.’ ELECTROPHORESIS, 8(1) pp. 38–44.

Vos, P., Hogers, R., Bleeker, M., Reijans, M., Lee, T. van de, Hornes, M., Friters, A., Pot, J., Paleman, J., Kuiper, M. and Zabeau, M. (1995) ‘AFLP: a new technique for DNA fingerprinting.’ Nucleic Acids Research, 23(21) pp. 4407–4414.

Osmosis

Osmosis is the diffusion of water or other solvents through a semipermeable membrane. First studied in 1877 in Germany it was discovered that water will move through a membrane to the area of higher concentration in order to dilute it. (osmosis | chemical process,)  A semi permeable membrane is a material that allows water and some other small minerals and materials but stops anything else passing through. Osmosis will always move solvents across the membrane from an area of low concentration to an area of high concentration, see (figure 1) In the end the pressure builds up and the osmosis will stop through osmoregulation. (science clarified)

osmosis
figure 1

Osmoregulation is a phycological process an organism uses to maintain water balance.  Mainly trying to keep concentration of body fluids outside of cells the same as it is on the inside. (Osmoregulation – Biology Encyclopaedia) This equilibrium helps to keep cells from either taking too much water and exploding or by letting to much go and shrivelling up.

Plant cells and animal cells are different so have different ways of comping with osmosis an osmoregulation. Plant cells have a thick cell wall and when places in a hypotonic solution the cell begins to swell but the cell wall prevents it from bursting. If a plant cell is put into a hypertonic solution, then the water from inside the cell will diffuse out and the cell will shrink. See (figure 2)

osmsis 2
figure 2

On the other hand, animal cells do not have this thick cell wall so when put into a hypotonic solution they can swell up ad burst. An organelle called contractile vacuoles are designed to prevent this from happening and they pump water out of the cell if this occurs. In hypertonic solutions water will diffuse out of the cell and the cell will shrink, however in animal’s cells are always surrounded by an isotonic solution which keeps equilibrium thus preventing the cell from shrinking. (The Effects of Osmosis)

 

The kidney is an organ an organ in which osmosis occurs, all mammals have kidneys and the function of this organ is to filter waste out of the blood.(How Your Kidneys Work, 2014)  Osmosis occurs in the kidneys and this helps to maintain and regulate salt and minerals in the blood. The first step is when molecules such as salts, urea, glucose and water diffuse from the glomerulus into a liquid within the bowman’s capsule. This is then all passes on to the proximal tubule, loop of Henle and then the distal tubule. There are loads of capillaries surrounding these three parts known as a nephron. See (figure 3) Water moves out of the tubules and loop on Henle and into the more concentrated are inside the capillaries.  If water is needed to be conserved even more then a hormone ADH is released; it makes the walls of the collection duct permeable to water so that it can be diffused in order to conserve. (Passive Transport)

osmosis 3
figure 3

Osmosis is being manipulated and used within industries to overcome issues in the world today. According to (Shaaban and Yahya, 2017) reverse osmosis is a technique that is currently considered the most reliable for brackish and sweater desalination. Hot countries such as Egypt require large amounts of desalinated water and the study being carried out by (Shaaban and Yahya) investigating the performance of reverse osmosis plants in hot climates. Fresh water can be obtained limitless supplies by desalinating seawater. Reverse osmosis was deemed the most effective way of producing freshwater however its disadvantage was that it needed a big energy supply.  Recent studies and investigations into this area of reverse osmosis and the industry have risen due to global energy crisis. The aim is to find and create a way of using less energy in reverse osmosis by using new technology. 

 

References

How Your Kidneys Work (2014) The National Kidney Foundation. [Online] [Accessed on 5th December 2017] https://www.kidney.org/kidneydisease/howkidneyswrk.

osmosis | chemical process (n.d.) Encyclopedia Britannica. [Online] [Accessed on 5th December 2017] https://www.britannica.com/science/osmosis.

Passive Transport (n.d.) The Kidney! [Online] [Accessed on 5th December 2017] http://kidneys-are-us.weebly.com/passive-transport.html.

Shaaban, S. and Yahya, H. (2017) ‘Detailed analysis of reverse osmosis systems in hot climate conditions.’ Desalination, 423, December, pp. 41–51.

The Effects of Osmosis (n.d.). [Online] [Accessed on 5th December 2017] http://www.etomica.org/app/modules/sites/Osmosis_old/Background1.html.

https://www.google.co.uk/search?q=osmosis&source=lnms&tbm=isch&sa=X&ved=0ahUKEwj7jZWgh_TXAhWIpqQKHbgcDnsQ_AUICigB&biw=1366&bih=662#imgrc=swcCZ-LyQakTOM:

https://www.google.co.uk/search?biw=1366&bih=662&tbm=isch&sa=1&ei=_y8nWpy6NMSXsAfTyJnwCQ&q=osmosis+in+kidneys&oq=osmosis+in+kid&gs_l=psy-ab.1.0.0j0i24k1l4

https://www.google.co.uk/search?biw=1366&bih=662&tbm=isch&sa=1&ei=LDAnWqSGLs2tkwWn84LoCg&q=hypertonic+hypotonic+isotonic&oq=hypertonic+h&gs_l=psy-ab.1.0.0l3j0i67k1j0l6.83363.89471.0.90798.30.17.0.2.2.0.169.1167.12j2.15.0….0…1c.1.64.psy-ab..16.13.965.0..0i24k1.88.hoHSv4wBvyQ#imgrc=cPLcPmEf9Pw4LM:

Advances in diagnosing and treating navicular diseases in horses.

The navicular bone is located in the lower heel of a horse just behind then coffin bone and the short pastern. (see figure 1) The navicular bone is prone to cause issues such as lameness in horses, navicular disease being one of these.

navicular
Figure 1 

Navicular disease is a progressive and degenerative condition involving the navicular bone.  (Navicular disease in horses: signs and treatment, 2001) Navicular is not classified as a disease in horses as it is just a series of abnormalities. Terms once used were “navicular syndrome” or “palmar foot pain” however due to advances in technology such as MRI scanning we now use the term to it as “navicular disease” to refer to changes in the navicular bone structure. The so called disease is stated to be one of the most common causes for severe can chronic lameness in horses. (Navicular Disease in Horses – Musculoskeletal System)

Diagnosing navicular disease can be quite tricky, but modern advances in technology have allowed it to be a little easier. MRI scanning allows us to look at soft tissue damage and fluid in addition to just the bone. Whereas in past times vets have had to take radiographs or which do not offer the insight of the soft tissues and supporting ligaments around the navicular bone itself. (The New Navicular Paradigm, 2016)

Since MRI scans have stared to be used they have shed a light on equine foot pathology and navicular dieses itself. If used correctly by an experienced MRI user then it can produce complex images and be used for a clear diagnostic; being able to tell specifically what is wrong with the horses foot/heel.(The New Navicular Paradigm, 2016)

We can see how technology advances had allowed us to be able to diagnose navicular disease in horses but now how have the industry advanced in ways of treating and preventing it?

In the past a horse owner’s wort nightmare would be to find out their horse had navicular disease; this is because there was no apparent cure and inevitably the horse would have an early retirement.  However, since MRI scans have been used vets and scientist could focus on specific areas and the root causes. In the summer of 2014 two new drugs were approved which would from then on help to combat and overcome navicular syndrome. (New options for navicular treatment, 2015) These two drugs are called Tildren and Osphos, they are both bisphosphonates and essentially work the same way and help with bone remodelling. (DVM, 2015)

Other advances in treating horses with navicular syndrome today can be rest, corrective shoeing, nerve blocks, and surgery. Shoeing Is a great way to treat it but must be done by an experienced farrier working closely with your vet.  Advances in remedial shoeing means farriers can fit “ egg bar”  shoes and/or pads which help to take weight of the heel and relieve tensions on the tendons. (Navicular Disease: Treatment and Prevention)

Prevention is always better than the cure. Preventing navicular disease isn’t too hard and could save a lot in the long run. All of these new treatments and diagnostics are effective and greatly appreciated in the industry however they come at a cost. Preventing navicular syndrome can be done by your horse receiving prober hoof care and shoeing and keeping an eye out for heat or swelling in the feet after strenuous work. Also keeping an eye of the hoofs for long toes, short heels or even uneven hoofs and getting this sorted and checked of if it occurs is good preventatives and shows good ownership too. (Navicular Disease: Treatment and Prevention)

 

References

DVM, K. M. (2015) Bisphosphonates and navicular syndrome in horses. dvm360.com. [Online] [Accessed on 21st November 2017] http://veterinarynews.dvm360.com/bisphosphonates-and-navicular-syndrome-horses.

Navicular Disease in Horses – Musculoskeletal System (n.d.) Veterinary Manual. [Online] [Accessed on 21st November 2017] https://www.msdvetmanual.com/musculoskeletal-system/lameness-in-horses/navicular-disease-in-horses.

Navicular disease in horses: signs and treatment (2001) Horse & Hound. [Online] [Accessed on 21st November 2017] http://www.horseandhound.co.uk/tag/navicular-disease.

Navicular Disease: Treatment and Prevention (n.d.) EquineSpot.com. [Online] [Accessed on 21st November 2017] http://www.equinespot.com/navicular-disease.html.

New options for navicular treatment (2015) The Horse Owner’s Resource. [Online] [Accessed on 21st November 2017] https://equusmagazine.com/diseases/options-navicular-treatment-28471.

The New Navicular Paradigm (2016) TheHorse.com. [Online] [Accessed on 21st November 2017] http://www.thehorse.com/articles/37431/the-new-navicular-paradigm.

Evaluation of blood metabolites reflects presence or absence of liver abscesses in beef cattle

 

 cow.png

(Alabama Beef Cattle Facts – Beef2Live, 2017)

 

Liver abscesses are a big concern at current time for the beef industry and its profitability. The abscesses contribute to bad health and performance of the cattle and can also be a threat to the beef market due to food safety; as some may go undetected during inspection. The chances and probability of cattle having liver abscesses and metabolic diseases is heightened in recent intensification of beef farming and some of the diets the cattle are put on. Where cattle are fed a diet with high-concentrate finishing rations with lower inclusion of roughage, it is calculated that between 12 and 32 percent of the cattle will have some form of metabolic disease or liver abscess. So far, the industry has lost hug amounts and apparently up to £30million annually in Canada.

It is quite hard to detect the liver abscesses before slaughter and attempts that have been done have always come back inconsistent.  Methods used to try and detect the abscesses before slaughter have been ones such as ultrasound and other diagnostic techniques. However as these are not proving accurate and giving inconsistent data there is defiantly a need for a new method. This method would need to detect the abscesses on the liver or any other metabolic diseases in a safe way for the cattle before slaughter. If such a method could be found then it would save the industry vast amount and would be able to draw up definite links to the liver abscesses and the way the cattle were fed, kept or even blood lines. This data and links would be able to be used to try and minimise the issue and maximise profit of the industry, along with animal health improvement.

Recent studies have suggested that

  • decrease in serum albumin
  • reduced blood testosterone
  • chronic active inflammation

are all connected and shown when liver abscesses are present. Using this information this study decided to look at bile and blood of cattle with suspected liver abscesses to pick up any correlation.

 

This study carried out an experiment using this information and monitored the blood and bile of cattle. They used twenty-nine beef cattle all within a specific weight and age range. They put all the cattle on a high- concentrate diet and collected blood at specific days but only stated 56 days before slaughter whereas the cattle were fed the diet 112 days before and this was the length of the experiment.

 

The experiment showed that after the trials  9 of the cattle had liver abscesses and that 20 didn’t. From the  blood results we could see that the 9 cattle with the liver abscess did have reduced testosterone, prolactin and even metabolic hormones such as cortisol and leptin.

We can now see that there is some form of correlation and although it  might not be a definite form of evidence it can still be used to try and  predict the outcome of  an abscess.

 

References

http://moodle.writtle.ac.uk/pluginfile.php/142606/mod_resource/content/1/blood%20metabolites%20beef%20cattle.pdf

Reflecting on maths and chemistry

Both maths and chemistry play an important part in the fundamentals in bio veterinary science module. It is important to have the correct basic understanding of this before moving on to more complex subjects and using this as a foundation. Before into Uni and starting this module, I had not done much with maths or chemistry so this was already going to be a weak spot. I was doing an equine course for the previous two years and had not been using my skills in the subjects very much unless it came up in subjects such as equine nutrition. The last time using maths and chemistry regularly would be when I was doing my GCSE’s at school, too which I can’t particularly remember much of.

So far in this module I have tried my hardest to try and pick things up and understand how to do the maths calculations. I have asked questions where necessary; trying to gain as much information as I can to help me understand how to complete my work. Some of the maths has confused me and I haven’t really understood the questions or where to start. To help myself get around this problem I have come up with a solution in which I plan to read up and study the area more and try out some online questions once I know the principles of the workings out. Using the website (Helmenstine and Ph.D., n.d.) I can help myself to understand maths for the biosciences better and hopefully be in a better position for the lessons in the future as I will have the foundation to fall back too.  A book that I found useful  too and that linked specially to the lectures was  called “core maths for the biosciences” (Reed, n.d.) This book has good examples and is clearly laid out. It was recommended during a lecture and is available in the Writtle library. I have had a look in it and took it out on loan finding it very useful for my studies.

Chemistry has never been my strongest subject o and I always seem to find it very daunting first. I seem to struggle when it comes to different compounds and the molecular structure. I haven’t found the chemistry in this module too difficult yet and have managed to keep up and understand what I am being taught, however I would like to do some personal studies and research to gather a better and more broad understanding and feel secure in myself; so that when things start to progress further in the module I am ready to approach it and have enough knowledge to build from and back up what is being discussed. I have found and online website which takes things down to the basics and builds up from there. (LabSkills for A Level Chemistry | Curriculum-focused e-learning science activities & support for students & teachers, n.d.)  I plan to use this for the time being to get myself back up to scratch with my chemistry and to a comfortable level.

 

 

My targets for the next few weeks and during study week are to get myself up to scratch with my maths and chemistry using the resources listed above and other ones which may be found during my studies. I hope to find strategic ways of learning and getting myself to the level I wish to be at within the next month. After this time, I want to be able to be comfortable answering and understating the maths questions given during lectures. I also hope to be at a level with my chemistry in such a way that I can start  to answer questions in lectures and that I have full understanding  of the molecular structure of the compounds being spoken about and how different chemicals bond and join together.

 

Reference list

 

Helmenstine, A. M. and Ph.D. (n.d.) Practice Calculating Concentration of Ions in an Aqueous Solution. ThoughtCo. [Online] [Accessed on 10th October 2017] https://www.thoughtco.com/calculate-concentration-of-ions-in-solution-609573.

LabSkills for A Level Chemistry | Curriculum-focused e-learning science activities & support for students & teachers (n.d.). [Online] [Accessed on 10th October 2017] http://www.labskills.co.uk/chemistry.php.

Reed, M. B. (n.d.) core maths for the biosciences.